rs11188067

Variant names:

• chr10-94733952-A-G
• rs11188067
• NM_000772.3:c.1291+514A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000772.3(CYP2C18):​c.1291+514A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 151,850 control chromosomes in the GnomAD database, including 3,251 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.20 (3251 hom., cov: 31)
• Consequence: CYP2C18 NM_000772.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 5 publications found

Genes affected

CYP2C18 (HGNC:2620): (cytochrome P450 family 2 subfamily C member 18) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein localizes to the endoplasmic reticulum but its specific substrate has not yet been determined. The gene is located within a cluster of cytochrome P450 genes on chromosome 10q24. An additional gene, CYP2C17, was once thought to exist; however, CYP2C17 is now considered an artefact based on a chimera of CYP2C18 and CYP2C19. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ENSG00000276490 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000772.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP2C18	NM_000772.3	MANE Select	c.1291+514A>G		intron	N/A	NP_000763.1
	CYP2C18	NM_001128925.2		c.1114+514A>G		intron	N/A	NP_001122397.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP2C18	ENST00000285979.11	TSL:1 MANE Select	c.1291+514A>G		intron	N/A	ENSP00000285979.6
	CYP2C18	ENST00000339022.6	TSL:1	c.1114+514A>G		intron	N/A	ENSP00000341293.5
	ENSG00000276490	ENST00000464755.1	TSL:2	n.931+514A>G		intron	N/A	ENSP00000483243.1

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30458 AN: 151732 Hom.: 3250 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.00947

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.202

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.201 AC: 30460 AN: 151850 Hom.: 3251 Cov.: 31 AF XY: 0.197 AC XY: 14621 AN XY: 74188

African (AFR) AF: 0.223 AC: 9260 AN: 41432

American (AMR) AF: 0.133 AC: 2020 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 739 AN: 3462

East Asian (EAS) AF: 0.00950 AC: 49 AN: 5160

South Asian (SAS) AF: 0.163 AC: 782 AN: 4800

European-Finnish (FIN) AF: 0.185 AC: 1957 AN: 10568

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.220 AC: 14923 AN: 67906

Other (OTH) AF: 0.200 AC: 421 AN: 2104

Alfa AF: 0.208 Hom.: 5641

Bravo AF: 0.197

Asia WGS AF: 0.0850 AC: 297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.79
DANN	Benign	0.53
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11188067; hg19: chr10-96493709;